---
_id: '12158'
abstract:
- lang: eng
text: 'Post-translational histone modifications modulate chromatin activity to affect
gene expression. How chromatin states underlie lineage choice in single cells
is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage
(sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3)
histone modifications in the mouse bone marrow. During differentiation, hematopoietic
stem and progenitor cells (HSPCs) acquire active chromatin states mediated by
cell-type-specifying transcription factors, which are unique for each lineage.
By contrast, most alterations in repressive marks during differentiation occur
independent of the final cell type. Chromatin trajectory analysis shows that lineage
choice at the chromatin level occurs at the progenitor stage. Joint profiling
of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage
have distinct active chromatin but share similar myeloid-specific heterochromatin
states. This implies a hierarchical regulation of chromatin during hematopoiesis:
heterochromatin dynamics distinguish differentiation trajectories and lineages,
while euchromatin dynamics reflect cell types within lineages.'
acknowledgement: We thank A. Giladi for sharing mRNA abundance tables of cell types
together with J. van den Berg for critical reading of the manuscript. We thank M.
Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich
Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973).
Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström
under CC-BY-SA 3.0 license. This work was supported by European Research Council
Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991),
HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z.
The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF
(ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. The funders had no role in study
design, data collection and analysis, decision to publish or preparation of the
manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Helena
full_name: Viñas Gaza, Helena
last_name: Viñas Gaza
- first_name: Buys Anton
full_name: de Barbanson, Buys Anton
last_name: de Barbanson
- first_name: Vivek
full_name: Bhardwaj, Vivek
last_name: Bhardwaj
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Reinier
full_name: van der Linden, Reinier
last_name: van der Linden
- first_name: Alexander
full_name: van Oudenaarden, Alexander
last_name: van Oudenaarden
citation:
ama: Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345.
doi:10.1038/s41588-022-01260-3
apa: Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu,
M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature.
https://doi.org/10.1038/s41588-022-01260-3
chicago: Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson,
Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden.
“Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.”
Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.
ieee: P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin
dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature,
pp. 333–345, 2023.
ista: Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M,
van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.
mla: Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin
Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature,
2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.
short: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu,
R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T07:48:24Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
file:
- access_level: open_access
checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:46:45Z
date_updated: 2023-02-27T07:46:45Z
file_id: '12688'
file_name: 2023_NatureGenetics_Zeller.pdf
file_size: 21484855
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:46:45Z
has_accepted_license: '1'
intvolume: ' 55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '12676'
abstract:
- lang: eng
text: Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum
games played on directed graphs with probabilistic transitions. The goal of player-max
is to maximize the probability to reach a target state against the adversarial
player-min. These games lie in NP ∩ coNP and are among the rare combinatorial
problems that belong to this complexity class for which the existence of polynomial-time
algorithm is a major open question. While randomized sub-exponential time algorithm
exists, all known deterministic algorithms require exponential time in the worst-case.
An important open question has been whether faster algorithms can be obtained
parametrized by the treewidth of the game graph. Even deterministic sub-exponential
time algorithm for constant treewidth turn-based stochastic games has remain elusive.
In this work our main result is a deterministic algorithm to solve turn-based
stochastic games that, given a game with n states, treewidth at most t, and the
bit-complexity of the probabilistic transition function log D, has running time
O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time
for games with constant or poly-logarithmic treewidth.
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt)
grant.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
citation:
ama: 'Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm
for turn-based stochastic games with bounded treewidth. In: Proceedings of
the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial
and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173'
apa: 'Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J.
(2023). Faster algorithm for turn-based stochastic games with bounded treewidth.
In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics.
https://doi.org/10.1137/1.9781611977554.ch173'
chicago: Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta,
and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded
Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete
Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023.
https://doi.org/10.1137/1.9781611977554.ch173.
ieee: K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster
algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy,
2023, pp. 4590–4605.
ista: 'Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster
algorithm for turn-based stochastic games with bounded treewidth. Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
on Discrete Algorithms, 4590–4605.'
mla: Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic
Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023,
pp. 4590–605, doi:10.1137/1.9781611977554.ch173.
short: K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings
of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial
and Applied Mathematics, 2023, pp. 4590–4605.
conference:
end_date: 2023-01-25
location: Florence, Italy
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2023-01-22
date_created: 2023-02-24T12:20:47Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T09:01:16Z
day: '01'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1137/1.9781611977554.ch173
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1137/1.9781611977554.ch173
month: '02'
oa: 1
oa_version: Published Version
page: 4590-4605
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611977554'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
status: public
title: Faster algorithm for turn-based stochastic games with bounded treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12735'
abstract:
- lang: eng
text: "Asynchronous programming has gained significant popularity over the last
decade: support for this programming pattern is available in many popular languages
via libraries and native language implementations, typically in the form of coroutines
or the async/await construct. Instead of programming via shared memory, this concept
assumes implicit synchronization through message passing. The key data structure
enabling such communication is the rendezvous channel. Roughly, a rendezvous channel
is a blocking queue of size zero, so both send(e) and receive() operations wait
for each other, performing a rendezvous when they meet. To optimize the message
passing pattern, channels are usually equipped with a fixed-size buffer, so sends
do not suspend and put elements into the buffer until its capacity is exceeded.
This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast
and scalable algorithm for both rendezvous and buffered channels. Similarly to
modern queues, our solution is based on an infinite array with two positional
counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add
instruction to update them. Yet, the algorithm requires non-trivial modifications
of this classic pattern, in order to support the full channel semantics, such
as buffering and cancellation of waiting requests. We compare the performance
of our solution to that of the Kotlin implementation, as well as against other
academic proposals, showing up to 9.8× speedup. To showcase its expressiveness
and performance, we also integrated the proposed algorithm into the standard Kotlin
Coroutines library, replacing the previous channel implementations."
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: 'Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines.
In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481'
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels
in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada:
Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable
Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, 107–18. Association for
Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in
Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.
ista: 'Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin
Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel
Programming, 107–118.'
mla: Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481.
short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Association for
Computing Machinery, 2023, pp. 107–118.
conference:
end_date: 2023-03-01
location: Montreal, QC, Canada
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2023-02-25
date_created: 2023-03-19T23:00:58Z
date_published: 2023-02-25T00:00:00Z
date_updated: 2023-03-20T07:29:28Z
day: '25'
department:
- _id: DaAl
doi: 10.1145/3572848.3577481
external_id:
arxiv:
- '2211.04986'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04986
month: '02'
oa: 1
oa_version: Preprint
page: 107-118
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9798400700156'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and scalable channels in Kotlin Coroutines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12736'
abstract:
- lang: eng
text: Although a wide variety of handcrafted concurrent data structures have been
proposed, there is considerable interest in universal approaches (Universal Constructions
or UCs) for building concurrent data structures. UCs (semi-)automatically convert
a sequential data structure into a concurrent one. The simplest approach uses
locks [3, 6] that protect a sequential data structure and allow only one process
to access it at a time. However, the resulting data structure is blocking. Most
work on UCs instead focuses on obtaining non-blocking progress guarantees such
as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have
appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware
UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et
al.
acknowledgement: 'This work was supported by: the Natural Sciences and Engineering
Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and
the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with
equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.'
article_processing_charge: No
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Ilya
full_name: Kokorin, Ilya
last_name: Kokorin
citation:
ama: Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying
Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512
apa: 'Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected
scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming (pp. 438–440). Montreal,
QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512'
chicago: Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected
Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. Association for Computing
Machinery, 2023. https://doi.org/10.1145/3572848.3577512.
ieee: V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling
in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.
ista: Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path
copying trees, Association for Computing Machinery,p.
mla: Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.
short: V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path
Copying Trees, Association for Computing Machinery, 2023.
conference:
end_date: 2023-03-01
location: Montreal, QB, Canada
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2023-02-25
date_created: 2023-03-19T23:00:58Z
date_published: 2023-02-25T00:00:00Z
date_updated: 2023-03-20T07:57:27Z
day: '25'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1145/3572848.3577512
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3572848.3577512
month: '02'
oa: 1
oa_version: Published Version
page: 438-440
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9798400700156'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Unexpected scaling in path copying trees
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12760'
abstract:
- lang: eng
text: "Dynamic programming (DP) is one of the fundamental paradigms in algorithm
design. However,\r\nmany DP algorithms have to fill in large DP tables, represented
by two-dimensional arrays, which causes at least quadratic running times and space
usages. This has led to the development of improved algorithms for special cases
when the DPs satisfy additional properties like, e.g., the Monge property or total
monotonicity.\r\nIn this paper, we consider a new condition which assumes (among
some other technical assumptions) that the rows of the DP table are monotone.
Under this assumption, we introduce\r\na novel data structure for computing (1
+ ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting,
and with polylogarithmic update times when the DP entries change\r\ndynamically.
To the best of our knowledge, our new condition is incomparable to previous conditions
and is the first which allows to derive dynamic algorithms based on existing DPs.
Instead of using two-dimensional arrays to store the DP tables, we store the rows
of the DP tables using monotone piecewise constant functions. This allows us to
store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits,
and to perform operations, such as (min, +)-convolution or rounding, on these
functions in polylogarithmic time.\r\nWe further present several applications
of our data structure. For bicriteria versions of k-balanced graph partitioning
and simultaneous source location, we obtain the first dynamic algorithms with
subpolynomial update times, as well as the first static algorithms using only
near-linear time and space. Additionally, we obtain the currently fastest algorithm
for fully dynamic knapsack."
acknowledgement: "Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research
is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA
project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science
Fund (FWF) project I 5025-N (DELTA), 2020-2024."
alternative_title:
- LIPIcs
article_number: '36'
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan
full_name: Neumann, Stefan
last_name: Neumann
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone
dynamic programs and applications. In: 40th International Symposium on Theoretical
Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36'
apa: 'Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic
maintenance of monotone dynamic programs and applications. In 40th International
Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36'
chicago: Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic
Maintenance of Monotone Dynamic Programs and Applications.” In 40th International
Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.
ieee: M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance
of monotone dynamic programs and applications,” in 40th International Symposium
on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.
ista: 'Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of
monotone dynamic programs and applications. 40th International Symposium on Theoretical
Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer
Science, LIPIcs, vol. 254, 36.'
mla: Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs
and Applications.” 40th International Symposium on Theoretical Aspects of Computer
Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.STACS.2023.36.
short: M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International
Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023.
conference:
end_date: 2023-03-09
location: Hamburg, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2023-03-07
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-03-27T06:46:27Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.STACS.2023.36
external_id:
arxiv:
- '2301.01744'
file:
- access_level: open_access
checksum: 22141ab8bc55188e2dfff665e5daecbd
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:37:22Z
date_updated: 2023-03-27T06:37:22Z
file_id: '12769'
file_name: 2023_LIPICS_HenzingerM.pdf
file_size: 872706
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:37:22Z
has_accepted_license: '1'
intvolume: ' 254'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: 40th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- '9783959772662'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maintenance of monotone dynamic programs and applications
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 254
year: '2023'
...
---
_id: '12716'
abstract:
- lang: eng
text: "The process of detecting and evaluating sensory information to guide behaviour
is termed perceptual decision-making (PDM), and is critical for the ability of
an organism to interact with its external world. Individuals with autism, a neurodevelopmental
condition primarily characterised by social and communication difficulties, frequently
exhibit altered sensory processing and PDM difficulties are widely reported. Recent
technological advancements have pushed forward our understanding of the genetic
changes accompanying this condition, however our understanding of how these mutations
affect the function of specific neuronal circuits and bring about the corresponding
behavioural changes remains limited. Here, we use an innate PDM task, the looming
avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality
across three molecularly distinct genetic mouse models of autism (Cul3, Setd5
and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli,
their responses are consistently delayed, requiring longer to initiate an appropriate
response than their wild-type siblings. Mutant animals show abnormal adaptation
in both their stimulus- evoked escape responses and exploratory dynamics following
repeated stimulus presentations. Similarly delayed behavioural responses are observed
in wild-type animals when faced with more ambiguous threats, suggesting the mutant
phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur
knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed
dissection of the neuronal mechanisms underlying the behavioural impairment. In
vivo extracellular recording revealed that visual responses were unaffected within
a key brain region for the rapid processing of visual threats, the superior colliculus
(SC), indicating that the behavioural delay was unlikely to originate from sensory
impairments. Delayed behavioural responses were recapitulated in the Setd5 model
following optogenetic stimulation of the excitatory output neurons of the SC,
which are known to mediate escape initiation through the activation of cells in
the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings
of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three
genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by
the misregulation of voltage-gated potassium channels. Overall, our results show
that the ability to use visual information to drive efficient escape responses
is impaired in three diverse genetic mouse models of autism and that, in one of
the models studied, this behavioural delay likely originates from differences
in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore,
this work showcases the use of an innate behavioural paradigm to mechanistically
dissect PDM processes in autism."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Burnett, Laura
id: 3B717F68-F248-11E8-B48F-1D18A9856A87
last_name: Burnett
orcid: 0000-0002-8937-410X
citation:
ama: Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate
rapid perceptual decision-making through subcortical circuits in mouse models
of autism. 2023. doi:10.15479/at:ista:12716
apa: Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours
to investigate rapid perceptual decision-making through subcortical circuits in
mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716
chicago: Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours
to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in
Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.
ieee: L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to
investigate rapid perceptual decision-making through subcortical circuits in mouse
models of autism,” Institute of Science and Technology Austria, 2023.
ista: Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours
to investigate rapid perceptual decision-making through subcortical circuits in
mouse models of autism. Institute of Science and Technology Austria.
mla: Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours
to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in
Mouse Models of Autism. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:12716.
short: L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to
Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse
Models of Autism, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-08T15:19:45Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-04-05T10:59:04Z
day: '10'
ddc:
- '599'
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:12716
ec_funded: 1
file:
- access_level: closed
checksum: 6c6d9cc2c4cdacb74e6b1047a34d7332
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lburnett
date_created: 2023-03-08T15:08:46Z
date_updated: 2023-03-08T15:08:46Z
file_id: '12717'
file_name: Burnett_Thesis_2023.docx
file_size: 23029260
relation: source_file
- access_level: open_access
checksum: cebc77705288bf4382db9b3541483cd0
content_type: application/pdf
creator: lburnett
date_created: 2023-03-08T15:08:46Z
date_updated: 2023-03-08T15:08:46Z
file_id: '12718'
file_name: Burnett_Thesis_2023_pdfA.pdf
file_size: 11959869
relation: main_file
success: 1
file_date_updated: 2023-03-08T15:08:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '178'
project:
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
title: To flee, or not to flee? Using innate defensive behaviours to investigate rapid
perceptual decision-making through subcortical circuits in mouse models of autism
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12854'
abstract:
- lang: eng
text: "The main idea behind BUBAAK is to run multiple program analyses in parallel
and use runtime monitoring and enforcement to observe and control their progress
in real time. The analyses send information about (un)explored states of the program
and discovered invariants to a monitor. The monitor processes the received data
and can force an analysis to stop the search of certain program parts (which have
already been analyzed by other analyses), or to make it utilize a program invariant
found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange
between the monitor and the analyses was not yet completed, which is why BUBAAK
only ran several analyses in parallel, without any coordination. Still, BUBAAK
won the meta-category FalsificationOverall and placed very well in several other
(sub)-categories of the competition."
acknowledgement: This work was supported by the ERC-2020-AdG 10102009 grant.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers.
In: Tools and Algorithms for the Construction and Analysis of Systems.
Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of
program verifiers. In Tools and Algorithms for the Construction and Analysis
of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32'
chicago: 'Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of
Program Verifiers.” In Tools and Algorithms for the Construction and Analysis
of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.'
ieee: 'M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,”
in Tools and Algorithms for the Construction and Analysis of Systems, Paris,
France, 2023, vol. 13994, pp. 535–540.'
ista: 'Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers.
Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994,
535–540.'
mla: 'Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program
Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems,
vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.'
short: M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction
and Analysis of Systems, Springer Nature, 2023, pp. 535–540.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2023-04-22
date_created: 2023-04-20T08:22:53Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:02:43Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30820-8_32
ec_funded: 1
file:
- access_level: open_access
checksum: 120d2c2a38384058ad0630fdf8288312
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T06:58:36Z
date_updated: 2023-04-25T06:58:36Z
file_id: '12864'
file_name: 2023_LNCS_Chalupa.pdf
file_size: 16096413
relation: main_file
success: 1
file_date_updated: 2023-04-25T06:58:36Z
has_accepted_license: '1'
intvolume: ' 13994'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 535-540
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783031308208'
eissn:
- 1611-3349
isbn:
- '9783031308192'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Bubaak: Runtime monitoring of program verifiers'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13994
year: '2023'
...
---
_id: '12846'
abstract:
- lang: eng
text: We present a formula for the signed area of a spherical polygon via prequantization.
In contrast to the traditional formula based on the Gauss-Bonnet theorem that
requires measuring angles, the new formula mimics Green's theorem and is applicable
to a wider range of degenerate spherical curves and polygons.
acknowledgement: The authors acknowledge Chris Wojtan for his continuous support to
the present work through discussions and advice. The second author thanks Anna Sisak
for a fruitful discussion on prequantum bundles. This project was funded in part
by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).
article_number: '2303.14555'
article_processing_charge: No
author:
- first_name: Albert
full_name: Chern, Albert
last_name: Chern
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
citation:
ama: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv. doi:10.48550/arXiv.2303.14555
apa: Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via
prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555
chicago: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons
via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.
ieee: A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,”
arXiv. .
ista: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
arXiv, 2303.14555.
mla: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via
Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.
short: A. Chern, S. Ishida, ArXiv (n.d.).
date_created: 2023-04-18T19:16:06Z
date_published: 2023-03-25T00:00:00Z
date_updated: 2023-04-25T06:51:21Z
day: '25'
department:
- _id: GradSch
- _id: ChWo
doi: 10.48550/arXiv.2303.14555
external_id:
arxiv:
- '2303.14555'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2303.14555
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: arXiv
publication_status: submitted
status: public
title: Area formula for spherical polygons via prequantization
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12856'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort
third-party monitoring. In: Fundamental Approaches to Software Engineering.
Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches
to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer
Nature. https://doi.org/10.1007/978-3-031-30826-0_15'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
“Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental
Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware
for best-effort third-party monitoring,” in Fundamental Approaches to Software
Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware
for best-effort third-party monitoring. Fundamental Approaches to Software Engineering.
FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.'
mla: 'Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.”
Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature,
2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.'
short: M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental
Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2023-04-22
date_created: 2023-04-20T08:29:42Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2023-04-25T07:19:07Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30826-0_15
ec_funded: 1
file:
- access_level: open_access
checksum: 17a7c8e08be609cf2408d37ea55e322c
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T07:16:36Z
date_updated: 2023-04-25T07:16:36Z
file_id: '12865'
file_name: 2023_LNCS_ChalupaM.pdf
file_size: 580828
relation: main_file
success: 1
file_date_updated: 2023-04-25T07:16:36Z
has_accepted_license: '1'
intvolume: ' 13991'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 260-281
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eisbn:
- '9783031308260'
eissn:
- 1611-3349
isbn:
- '9783031308253'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12407'
relation: earlier_version
status: public
status: public
title: 'Vamos: Middleware for best-effort third-party monitoring'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13991
year: '2023'
...
---
_id: '12407'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\n\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions."
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for
Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria;
2023. doi:10.15479/AT:ISTA:12407'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware
for Best-Effort Third-Party Monitoring. Institute of Science and Technology
Austria, 2023.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware
for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria,
38p.'
mla: 'Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.'
short: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware
for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria,
2023.'
date_created: 2023-01-27T03:18:08Z
date_published: 2023-01-27T00:00:00Z
date_updated: 2023-04-25T07:19:06Z
day: '27'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:12407
ec_funded: 1
file:
- access_level: open_access
checksum: 55426e463fdeafe9777fc3ff635154c7
content_type: application/pdf
creator: fmuehlbo
date_created: 2023-01-27T03:18:34Z
date_updated: 2023-01-27T03:18:34Z
file_id: '12408'
file_name: main.pdf
file_size: 662409
relation: main_file
success: 1
file_date_updated: 2023-01-27T03:18:34Z
has_accepted_license: '1'
keyword:
- runtime monitoring
- best effort
- third party
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '38'
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
eissn:
- 2664-1690
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12856'
relation: later_version
status: public
status: public
title: 'VAMOS: Middleware for Best-Effort Third-Party Monitoring'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...